Tissue handling and specimen preparation in surgical pathology: issues concerning the recovery of nucleic acids from formalin-fixed, paraffin-embedded tissue

Arch Pathol Lab Med. 2008 Dec;132(12):1929-35. doi: 10.5858/132.12.1929.


Context: Expression profiling by microarrays and real-time polymerase chain reaction-based assays is a powerful tool for classification and prognostication of disease; however, it remains a research tool, largely reliant on frozen tissue. Limiting the utility of expression profiling is the isolation of quality nucleic acids from formalin-fixed, paraffin-embedded tissue. The collection, handling, and processing of tissue directly impacts the biomolecules that can be recovered from it. High-quality nucleic acids can be obtained from formalin-fixed, paraffin-embedded tissue, but greater attention to all steps in the process of tissue handling and preparation is required.

Objective: To summarize the current state-of-the-art of preanalytic factors in tissue handling and processing as they impact the quality of RNA obtainable from formalin-fixed, paraffin-embedded tissue. The goals are to provide recommendations that will improve RNA quality for expression profiling from formalin-fixed, paraffin-embedded tissue and highlight areas for additional research. Tissue is an analyte and it must be handled in a standardized fashion to provide consistent results.

Data sources: The literature was reviewed. Consultation with industry and academic leaders in the use of RNA for expression profiling was obtained to identify areas for additional research.

Conclusions: Development of RNA-based assays from formalin-fixed, paraffin-embedded tissue is feasible. Greater attention to tissue handling and processing is essential to improve the quality of biospecimens for the development of robust RNA-based assays. Standardization of procedures and vigorous testing of alternative protocols are required to ensure that these assays function as designed.

Publication types

  • Review

MeSH terms

  • Formaldehyde
  • Gene Expression Profiling / methods
  • Histocytological Preparation Techniques / methods
  • Humans
  • Nucleic Acids / analysis*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Paraffin Embedding
  • Pathology, Surgical / methods*
  • RNA / analysis
  • Specimen Handling / methods


  • Nucleic Acids
  • Formaldehyde
  • RNA